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%\preprint{AIP/123-QED} |
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\title{Real space alternatives to the Ewald |
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Sum. II. Comparison of Methods} % Force line breaks with \\ |
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\title{Real space electrostatics for multipoles. II. Comparisons with |
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the Ewald Sum} |
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\author{Madan Lamichhane} |
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\affiliation{Department of Physics, University |
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of Notre Dame, Notre Dame, IN 46556}%Lines break automatically or can be forced with \\ |
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\affiliation{Department of Physics, University of Notre Dame, Notre Dame, IN 46556} |
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\author{Kathie E. Newman} |
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\affiliation{Department of Physics, University |
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of Notre Dame, Notre Dame, IN 46556} |
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\affiliation{Department of Physics, University of Notre Dame, Notre Dame, IN 46556} |
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\author{J. Daniel Gezelter}% |
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\email{gezelter@nd.edu.} |
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\affiliation{Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556%\\This line break forced with \textbackslash\textbackslash |
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}% |
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\affiliation{Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556 |
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} |
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\date{\today}% It is always \today, today, |
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% but any date may be explicitly specified |
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\date{\today} |
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\begin{abstract} |
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We have tested the real-space shifted potential (SP), |
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gradient-shifted force (GSF), and Taylor-shifted force (TSF) methods |
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for multipoles that were developed in the first paper in this series |
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against a reference method. The tests were carried out in a variety |
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of condensed-phase environments which were designed to test all |
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levels of the multipole-multipole interactions. Comparisons of the |
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We report on tests of the shifted potential (SP), gradient shifted |
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force (GSF), and Taylor shifted force (TSF) real-space methods for |
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multipole interactions developed in the first paper in this series, |
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using the multipolar Ewald sum as a reference method. The tests were |
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carried out in a variety of condensed-phase environments designed to |
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test up to quadrupole-quadrupole interactions. Comparisons of the |
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energy differences between configurations, molecular forces, and |
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torques were used to analyze how well the real-space models perform |
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relative to the more computationally expensive Ewald sum. We have |
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also investigated the energy conservation properties of the new |
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methods in molecular dynamics simulations using all of these |
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methods. The SP method shows excellent agreement with |
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configurational energy differences, forces, and torques, and would |
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be suitable for use in Monte Carlo calculations. Of the two new |
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shifted-force methods, the GSF approach shows the best agreement |
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with Ewald-derived energies, forces, and torques and exhibits energy |
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conservation properties that make it an excellent choice for |
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efficiently computing electrostatic interactions in molecular |
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dynamics simulations. |
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relative to the more computationally expensive Ewald treatment. We |
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have also investigated the energy conservation properties of the new |
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methods in molecular dynamics simulations. The SP method shows |
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excellent agreement with configurational energy differences, forces, |
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and torques, and would be suitable for use in Monte Carlo |
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calculations. Of the two new shifted-force methods, the GSF |
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approach shows the best agreement with Ewald-derived energies, |
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forces, and torques and also exhibits energy conservation properties |
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that make it an excellent choice for efficient computation of |
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electrostatic interactions in molecular dynamics simulations. |
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\end{abstract} |
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|
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%\pacs{Valid PACS appear here}% PACS, the Physics and Astronomy |
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% Classification Scheme. |
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\keywords{Electrostatics, Multipoles, Real-space} |
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%\keywords{Electrostatics, Multipoles, Real-space} |
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|
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\maketitle |
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|
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– |
|
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\section{\label{sec:intro}Introduction} |
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|
Computing the interactions between electrostatic sites is one of the |
95 |
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most expensive aspects of molecular simulations, which is why there |
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have been significant efforts to develop practical, efficient and |
97 |
< |
convergent methods for handling these interactions. Ewald's method is |
98 |
< |
perhaps the best known and most accurate method for evaluating |
99 |
< |
energies, forces, and torques in explicitly-periodic simulation |
100 |
< |
cells. In this approach, the conditionally convergent electrostatic |
101 |
< |
energy is converted into two absolutely convergent contributions, one |
102 |
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which is carried out in real space with a cutoff radius, and one in |
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reciprocal space.\cite{Clarke:1986eu,Woodcock75} |
95 |
> |
most expensive aspects of molecular simulations. There have been |
96 |
> |
significant efforts to develop practical, efficient and convergent |
97 |
> |
methods for handling these interactions. Ewald's method is perhaps the |
98 |
> |
best known and most accurate method for evaluating energies, forces, |
99 |
> |
and torques in explicitly-periodic simulation cells. In this approach, |
100 |
> |
the conditionally convergent electrostatic energy is converted into |
101 |
> |
two absolutely convergent contributions, one which is carried out in |
102 |
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real space with a cutoff radius, and one in reciprocal |
103 |
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space.\cite{Ewald21,deLeeuw80,Smith81,Allen87} |
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|
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When carried out as originally formulated, the reciprocal-space |
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portion of the Ewald sum exhibits relatively poor computational |
107 |
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scaling, making it prohibitive for large systems. By utilizing |
108 |
< |
particle meshes and three dimensional fast Fourier transforms (FFT), |
109 |
< |
the particle-mesh Ewald (PME), particle-particle particle-mesh Ewald |
110 |
< |
(P\textsuperscript{3}ME), and smooth particle mesh Ewald (SPME) methods can decrease |
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< |
the computational cost from $O(N^2)$ down to $O(N \log |
112 |
< |
N)$.\cite{Takada93,Gunsteren94,Gunsteren95,Darden:1993pd,Essmann:1995pb}. |
107 |
> |
scaling, making it prohibitive for large systems. By utilizing a |
108 |
> |
particle mesh and three dimensional fast Fourier transforms (FFT), the |
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particle-mesh Ewald (PME), particle-particle particle-mesh Ewald |
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> |
(P\textsuperscript{3}ME), and smooth particle mesh Ewald (SPME) |
111 |
> |
methods can decrease the computational cost from $O(N^2)$ down to $O(N |
112 |
> |
\log |
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N)$.\cite{Takada93,Gunsteren94,Gunsteren95,Darden:1993pd,Essmann:1995pb} |
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|
|
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Because of the artificial periodicity required for the Ewald sum, the |
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method may require modification to compute interactions for |
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> |
Because of the artificial periodicity required for the Ewald sum, |
116 |
|
interfacial molecular systems such as membranes and liquid-vapor |
117 |
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interfaces.\cite{Parry:1975if,Parry:1976fq,Clarke77,Perram79,Rhee:1989kl} |
118 |
< |
To simulate interfacial systems, Parry's extension of the 3D Ewald sum |
119 |
< |
is appropriate for slab geometries.\cite{Parry:1975if} The inherent |
120 |
< |
periodicity in the Ewald’s method can also be problematic for |
121 |
< |
interfacial molecular systems.\cite{Fennell:2006lq} Modified Ewald |
122 |
< |
methods that were developed to handle two-dimensional (2D) |
123 |
< |
electrostatic interactions in interfacial systems have not had similar |
124 |
< |
particle-mesh treatments.\cite{Parry:1975if, Parry:1976fq, Clarke77, |
125 |
< |
Perram79,Rhee:1989kl,Spohr:1997sf,Yeh:1999oq} |
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> |
interfaces require modifications to the method. Parry's extension of |
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the three dimensional Ewald sum is appropriate for slab |
119 |
> |
geometries.\cite{Parry:1975if} Modified Ewald methods that were |
120 |
> |
developed to handle two-dimensional (2-D) electrostatic |
121 |
> |
interactions.\cite{Parry:1975if,Parry:1976fq,Clarke77,Perram79,Rhee:1989kl} |
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> |
These methods were originally quite computationally |
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> |
expensive.\cite{Spohr97,Yeh99} There have been several successful |
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efforts that reduced the computational cost of 2-D lattice summations, |
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> |
bringing them more in line with the scaling for the full 3-D |
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> |
treatments.\cite{Yeh99,Kawata01,Arnold02,deJoannis02,Brodka04} The |
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inherent periodicity required by the Ewald method can also be |
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problematic in a number of protein/solvent and ionic solution |
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> |
environments.\cite{Roberts94,Roberts95,Luty96,Hunenberger99a,Hunenberger99b,Weber00,Fennell:2006lq} |
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|
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|
\subsection{Real-space methods} |
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Wolf \textit{et al.}\cite{Wolf:1999dn} proposed a real space $O(N)$ |
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|
method for calculating electrostatic interactions between point |
134 |
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charges. They argued that the effective Coulomb interaction in |
135 |
< |
condensed systems is actually short ranged.\cite{Wolf92,Wolf95}. For |
136 |
< |
an ordered lattice (e.g., when computing the Madelung constant of an |
137 |
< |
ionic solid), the material can be considered as a set of ions |
138 |
< |
interacting with neutral dipolar or quadrupolar ``molecules'' giving |
139 |
< |
an effective distance dependence for the electrostatic interactions of |
140 |
< |
$r^{-5}$ (see figure \ref{fig:NaCl}). For this reason, careful |
141 |
< |
applications of Wolf's method are able to obtain accurate estimates of |
142 |
< |
Madelung constants using relatively short cutoff radii. Recently, |
143 |
< |
Fukuda used neutralization of the higher order moments for the |
144 |
< |
calculation of the electrostatic interaction of the point charges |
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< |
system.\cite{Fukuda:2013sf} |
134 |
> |
charges. They argued that the effective Coulomb interaction in most |
135 |
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condensed phase systems is effectively short |
136 |
> |
ranged.\cite{Wolf92,Wolf95} For an ordered lattice (e.g., when |
137 |
> |
computing the Madelung constant of an ionic solid), the material can |
138 |
> |
be considered as a set of ions interacting with neutral dipolar or |
139 |
> |
quadrupolar ``molecules'' giving an effective distance dependence for |
140 |
> |
the electrostatic interactions of $r^{-5}$ (see figure |
141 |
> |
\ref{fig:schematic}). If one views the \ce{NaCl} crystal as a simple |
142 |
> |
cubic (SC) structure with an octupolar \ce{(NaCl)4} basis, the |
143 |
> |
electrostatic energy per ion converges more rapidly to the Madelung |
144 |
> |
energy than the dipolar approximation.\cite{Wolf92} To find the |
145 |
> |
correct Madelung constant, Lacman suggested that the NaCl structure |
146 |
> |
could be constructed in a way that the finite crystal terminates with |
147 |
> |
complete \ce{(NaCl)4} molecules.\cite{Lacman65} The central ion sees |
148 |
> |
what is effectively a set of octupoles at large distances. These facts |
149 |
> |
suggest that the Madelung constants are relatively short ranged for |
150 |
> |
perfect ionic crystals.\cite{Wolf:1999dn} For this reason, careful |
151 |
> |
application of Wolf's method can provide accurate estimates of |
152 |
> |
Madelung constants using relatively short cutoff radii. |
153 |
|
|
154 |
< |
\begin{figure}[h!] |
154 |
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Direct truncation of interactions at a cutoff radius creates numerical |
155 |
> |
errors. Wolf \textit{et al.} suggest that truncation errors are due |
156 |
> |
to net charge remaining inside the cutoff sphere.\cite{Wolf:1999dn} To |
157 |
> |
neutralize this charge they proposed placing an image charge on the |
158 |
> |
surface of the cutoff sphere for every real charge inside the cutoff. |
159 |
> |
These charges are present for the evaluation of both the pair |
160 |
> |
interaction energy and the force, although the force expression |
161 |
> |
maintains a discontinuity at the cutoff sphere. In the original Wolf |
162 |
> |
formulation, the total energy for the charge and image were not equal |
163 |
> |
to the integral of the force expression, and as a result, the total |
164 |
> |
energy would not be conserved in molecular dynamics (MD) |
165 |
> |
simulations.\cite{Zahn:2002hc} Zahn \textit{et al.}, and Fennel and |
166 |
> |
Gezelter later proposed shifted force variants of the Wolf method with |
167 |
> |
commensurate force and energy expressions that do not exhibit this |
168 |
> |
problem.\cite{Zahn:2002hc,Fennell:2006lq} Related real-space methods |
169 |
> |
were also proposed by Chen \textit{et |
170 |
> |
al.}\cite{Chen:2004du,Chen:2006ii,Denesyuk:2008ez,Rodgers:2006nw} |
171 |
> |
and by Wu and Brooks.\cite{Wu:044107} Recently, Fukuda has successfuly |
172 |
> |
used additional neutralization of higher order moments for systems of |
173 |
> |
point charges.\cite{Fukuda:2013sf} |
174 |
> |
|
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> |
\begin{figure} |
176 |
|
\centering |
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\includegraphics[width=0.50 \textwidth]{chargesystem.pdf} |
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\caption{Top: NaCl crystal showing how spherical truncation can |
179 |
< |
breaking effective charge ordering, and how complete \ce{(NaCl)4} |
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molecules interact with the central ion. Bottom: A dipolar |
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< |
crystal exhibiting similar behavior and illustrating how the |
182 |
< |
effective dipole-octupole interactions can be disrupted by |
183 |
< |
spherical truncation.} |
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\label{fig:NaCl} |
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\includegraphics[width=\linewidth]{schematic.eps} |
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> |
\caption{Top: Ionic systems exhibit local clustering of dissimilar |
179 |
> |
charges (in the smaller grey circle), so interactions are |
180 |
> |
effectively charge-multipole at longer distances. With hard |
181 |
> |
cutoffs, motion of individual charges in and out of the cutoff |
182 |
> |
sphere can break the effective multipolar ordering. Bottom: |
183 |
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dipolar crystals and fluids have a similar effective |
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\textit{quadrupolar} ordering (in the smaller grey circles), and |
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> |
orientational averaging helps to reduce the effective range of the |
186 |
> |
interactions in the fluid. Placement of reversed image multipoles |
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> |
on the surface of the cutoff sphere recovers the effective |
188 |
> |
higher-order multipole behavior.} |
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> |
\label{fig:schematic} |
190 |
|
\end{figure} |
191 |
|
|
192 |
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The direct truncation of interactions at a cutoff radius creates |
193 |
< |
truncation defects. Wolf \textit{et al.} further argued that |
194 |
< |
truncation errors are due to net charge remaining inside the cutoff |
195 |
< |
sphere.\cite{Wolf:1999dn} To neutralize this charge they proposed |
196 |
< |
placing an image charge on the surface of the cutoff sphere for every |
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< |
real charge inside the cutoff. These charges are present for the |
198 |
< |
evaluation of both the pair interaction energy and the force, although |
199 |
< |
the force expression maintained a discontinuity at the cutoff sphere. |
200 |
< |
In the original Wolf formulation, the total energy for the charge and |
201 |
< |
image were not equal to the integral of their force expression, and as |
170 |
< |
a result, the total energy would not be conserved in molecular |
171 |
< |
dynamics (MD) simulations.\cite{Zahn:2002hc} Zahn \textit{et al.} and |
172 |
< |
Fennel and Gezelter later proposed shifted force variants of the Wolf |
173 |
< |
method with commensurate force and energy expressions that do not |
174 |
< |
exhibit this problem.\cite{Fennell:2006lq} Related real-space |
175 |
< |
methods were also proposed by Chen \textit{et |
176 |
< |
al.}\cite{Chen:2004du,Chen:2006ii,Denesyuk:2008ez,Rodgers:2006nw} |
177 |
< |
and by Wu and Brooks.\cite{Wu:044107} |
178 |
< |
|
179 |
< |
Considering the interaction of one central ion in an ionic crystal |
180 |
< |
with a portion of the crystal at some distance, the effective Columbic |
181 |
< |
potential is found to be decreasing as $r^{-5}$. If one views the |
182 |
< |
\ce{NaCl} crystal as simple cubic (SC) structure with an octupolar |
183 |
< |
\ce{(NaCl)4} basis, the electrostatic energy per ion converges more |
184 |
< |
rapidly to the Madelung energy than the dipolar |
185 |
< |
approximation.\cite{Wolf92} To find the correct Madelung constant, |
186 |
< |
Lacman suggested that the NaCl structure could be constructed in a way |
187 |
< |
that the finite crystal terminates with complete \ce{(NaCl)4} |
188 |
< |
molecules.\cite{Lacman65} Any charge in a NaCl crystal is surrounded |
189 |
< |
by opposite charges. Similarly for each pair of charges, there is an |
190 |
< |
opposite pair of charge adjacent to it. The central ion sees what is |
191 |
< |
effectively a set of octupoles at large distances. These facts suggest |
192 |
< |
that the Madelung constants are relatively short ranged for perfect |
193 |
< |
ionic crystals.\cite{Wolf:1999dn} |
194 |
< |
|
195 |
< |
One can make a similar argument for crystals of point multipoles. The |
196 |
< |
Luttinger and Tisza treatment of energy constants for dipolar lattices |
197 |
< |
utilizes 24 basis vectors that contain dipoles at the eight corners of |
198 |
< |
a unit cube. Only three of these basis vectors, $X_1, Y_1, |
199 |
< |
\mathrm{~and~} Z_1,$ retain net dipole moments, while the rest have |
200 |
< |
zero net dipole and retain contributions only from higher order |
201 |
< |
multipoles. The effective interaction between a dipole at the center |
192 |
> |
One can make a similar effective range argument for crystals of point |
193 |
> |
\textit{multipoles}. The Luttinger and Tisza treatment of energy |
194 |
> |
constants for dipolar lattices utilizes 24 basis vectors that contain |
195 |
> |
dipoles at the eight corners of a unit cube.\cite{LT} Only three of |
196 |
> |
these basis vectors, $X_1, Y_1, \mathrm{~and~} Z_1,$ retain net dipole |
197 |
> |
moments, while the rest have zero net dipole and retain contributions |
198 |
> |
only from higher order multipoles. The lowest-energy crystalline |
199 |
> |
structures are built out of basis vectors that have only residual |
200 |
> |
quadrupolar moments (e.g. the $Z_5$ array). In these low energy |
201 |
> |
structures, the effective interaction between a dipole at the center |
202 |
|
of a crystal and a group of eight dipoles farther away is |
203 |
|
significantly shorter ranged than the $r^{-3}$ that one would expect |
204 |
|
for raw dipole-dipole interactions. Only in crystals which retain a |
208 |
|
unstable. |
209 |
|
|
210 |
|
In ionic crystals, real-space truncation can break the effective |
211 |
< |
multipolar arrangements (see Fig. \ref{fig:NaCl}), causing significant |
212 |
< |
swings in the electrostatic energy as individual ions move back and |
213 |
< |
forth across the boundary. This is why the image charges are |
211 |
> |
multipolar arrangements (see Fig. \ref{fig:schematic}), causing |
212 |
> |
significant swings in the electrostatic energy as individual ions move |
213 |
> |
back and forth across the boundary. This is why the image charges are |
214 |
|
necessary for the Wolf sum to exhibit rapid convergence. Similarly, |
215 |
|
the real-space truncation of point multipole interactions breaks |
216 |
|
higher order multipole arrangements, and image multipoles are required |
217 |
|
for real-space treatments of electrostatic energies. |
218 |
+ |
|
219 |
+ |
The shorter effective range of electrostatic interactions is not |
220 |
+ |
limited to perfect crystals, but can also apply in disordered fluids. |
221 |
+ |
Even at elevated temperatures, there is local charge balance in an |
222 |
+ |
ionic liquid, where each positive ion has surroundings dominated by |
223 |
+ |
negaitve ions and vice versa. The reversed-charge images on the |
224 |
+ |
cutoff sphere that are integral to the Wolf and DSF approaches retain |
225 |
+ |
the effective multipolar interactions as the charges traverse the |
226 |
+ |
cutoff boundary. |
227 |
+ |
|
228 |
+ |
In multipolar fluids (see Fig. \ref{fig:schematic}) there is |
229 |
+ |
significant orientational averaging that additionally reduces the |
230 |
+ |
effect of long-range multipolar interactions. The image multipoles |
231 |
+ |
that are introduced in the TSF, GSF, and SP methods mimic this effect |
232 |
+ |
and reduce the effective range of the multipolar interactions as |
233 |
+ |
interacting molecules traverse each other's cutoff boundaries. |
234 |
|
|
235 |
|
% Because of this reason, although the nature of electrostatic |
236 |
|
% interaction short ranged, the hard cutoff sphere creates very large |
242 |
|
% to the non-neutralized value of the higher order moments within the |
243 |
|
% cutoff sphere. |
244 |
|
|
245 |
< |
The forces and torques acting on atomic sites are the fundamental |
246 |
< |
factors driving dynamics in molecular simulations. Fennell and |
247 |
< |
Gezelter proposed the damped shifted force (DSF) energy kernel to |
248 |
< |
obtain consistent energies and forces on the atoms within the cutoff |
249 |
< |
sphere. Both the energy and the force go smoothly to zero as an atom |
250 |
< |
aproaches the cutoff radius. The comparisons of the accuracy these |
251 |
< |
quantities between the DSF kernel and SPME was surprisingly |
252 |
< |
good.\cite{Fennell:2006lq} The DSF method has seen increasing use for |
253 |
< |
calculating electrostatic interactions in molecular systems with |
254 |
< |
relatively uniform charge |
239 |
< |
densities.\cite{Shi:2013ij,Kannam:2012rr,Acevedo13,Space12,English08,Lawrence13,Vergne13} |
245 |
> |
Forces and torques acting on atomic sites are fundamental in driving |
246 |
> |
dynamics in molecular simulations, and the damped shifted force (DSF) |
247 |
> |
energy kernel provides consistent energies and forces on charged atoms |
248 |
> |
within the cutoff sphere. Both the energy and the force go smoothly to |
249 |
> |
zero as an atom aproaches the cutoff radius. The comparisons of the |
250 |
> |
accuracy these quantities between the DSF kernel and SPME was |
251 |
> |
surprisingly good.\cite{Fennell:2006lq} As a result, the DSF method |
252 |
> |
has seen increasing use in molecular systems with relatively uniform |
253 |
> |
charge |
254 |
> |
densities.\cite{English08,Kannam:2012rr,Space12,Lawrence13,Acevedo13,Shi:2013ij,Vergne13} |
255 |
|
|
256 |
|
\subsection{The damping function} |
257 |
< |
The damping function used in our research has been discussed in detail |
258 |
< |
in the first paper of this series.\cite{PaperI} The radial kernel |
259 |
< |
$1/r$ for the interactions between point charges can be replaced by |
260 |
< |
the complementary error function $\mathrm{erfc}(\alpha r)/r$ to |
261 |
< |
accelerate the rate of convergence, where $\alpha$ is a damping |
262 |
< |
parameter with units of inverse distance. Altering the value of |
263 |
< |
$\alpha$ is equivalent to changing the width of Gaussian charge |
264 |
< |
distributions that replace each point charge -- Gaussian overlap |
265 |
< |
integrals yield complementary error functions when truncated at a |
266 |
< |
finite distance. |
257 |
> |
The damping function has been discussed in detail in the first paper |
258 |
> |
of this series.\cite{PaperI} The $1/r$ Coulombic kernel for the |
259 |
> |
interactions between point charges can be replaced by the |
260 |
> |
complementary error function $\mathrm{erfc}(\alpha r)/r$ to accelerate |
261 |
> |
convergence, where $\alpha$ is a damping parameter with units of |
262 |
> |
inverse distance. Altering the value of $\alpha$ is equivalent to |
263 |
> |
changing the width of Gaussian charge distributions that replace each |
264 |
> |
point charge, as Coulomb integrals with Gaussian charge distributions |
265 |
> |
produce complementary error functions when truncated at a finite |
266 |
> |
distance. |
267 |
|
|
268 |
< |
By using suitable value of damping alpha ($\alpha \sim 0.2$) for a |
269 |
< |
cutoff radius ($r_{Âc}=9 A$), Fennel and Gezelter produced very good |
270 |
< |
agreement with SPME for the interaction energies, forces and torques |
271 |
< |
for charge-charge interactions.\cite{Fennell:2006lq} |
268 |
> |
With moderate damping coefficients, $\alpha \sim 0.2$, the DSF method |
269 |
> |
produced very good agreement with SPME for interaction energies, |
270 |
> |
forces and torques for charge-charge |
271 |
> |
interactions.\cite{Fennell:2006lq} |
272 |
|
|
273 |
|
\subsection{Point multipoles in molecular modeling} |
274 |
|
Coarse-graining approaches which treat entire molecular subsystems as |
275 |
|
a single rigid body are now widely used. A common feature of many |
276 |
|
coarse-graining approaches is simplification of the electrostatic |
277 |
|
interactions between bodies so that fewer site-site interactions are |
278 |
< |
required to compute configurational energies. Many coarse-grained |
279 |
< |
molecular structures would normally consist of equal positive and |
265 |
< |
negative charges, and rather than use multiple site-site interactions, |
266 |
< |
the interaction between higher order multipoles can also be used to |
267 |
< |
evaluate a single molecule-molecule |
268 |
< |
interaction.\cite{Ren06,Essex10,Essex11} |
278 |
> |
required to compute configurational |
279 |
> |
energies.\cite{Ren06,Essex10,Essex11} |
280 |
|
|
281 |
< |
Because electrons in a molecule are not localized at specific points, |
282 |
< |
the assignment of partial charges to atomic centers is a relatively |
283 |
< |
rough approximation. Atomic sites can also be assigned point |
284 |
< |
multipoles and polarizabilities to increase the accuracy of the |
285 |
< |
molecular model. Recently, water has been modeled with point |
286 |
< |
multipoles up to octupolar order using the soft sticky |
276 |
< |
dipole-quadrupole-octupole (SSDQO) |
281 |
> |
Additionally, because electrons in a molecule are not localized at |
282 |
> |
specific points, the assignment of partial charges to atomic centers |
283 |
> |
is always an approximation. For increased accuracy, atomic sites can |
284 |
> |
also be assigned point multipoles and polarizabilities. Recently, |
285 |
> |
water has been modeled with point multipoles up to octupolar order |
286 |
> |
using the soft sticky dipole-quadrupole-octupole (SSDQO) |
287 |
|
model.\cite{Ichiye10_1,Ichiye10_2,Ichiye10_3} Atom-centered point |
288 |
|
multipoles up to quadrupolar order have also been coupled with point |
289 |
|
polarizabilities in the high-quality AMOEBA and iAMOEBA water |
290 |
< |
models.\cite{Ren:2003uq,Ren:2004kx,Ponder:2010vl,Wang:2013fk} But |
291 |
< |
using point multipole with the real space truncation without |
292 |
< |
accounting for multipolar neutrality will create energy conservation |
293 |
< |
issues in molecular dynamics (MD) simulations. |
290 |
> |
models.\cite{Ren:2003uq,Ren:2004kx,Ponder:2010vl,Wang:2013fk} However, |
291 |
> |
truncating point multipoles without smoothing the forces and torques |
292 |
> |
can create energy conservation issues in molecular dynamics |
293 |
> |
simulations. |
294 |
|
|
295 |
|
In this paper we test a set of real-space methods that were developed |
296 |
|
for point multipolar interactions. These methods extend the damped |
297 |
|
shifted force (DSF) and Wolf methods originally developed for |
298 |
|
charge-charge interactions and generalize them for higher order |
299 |
< |
multipoles. The detailed mathematical development of these methods has |
300 |
< |
been presented in the first paper in this series, while this work |
301 |
< |
covers the testing the energies, forces, torques, and energy |
299 |
> |
multipoles. The detailed mathematical development of these methods |
300 |
> |
has been presented in the first paper in this series, while this work |
301 |
> |
covers the testing of energies, forces, torques, and energy |
302 |
|
conservation properties of the methods in realistic simulation |
303 |
|
environments. In all cases, the methods are compared with the |
304 |
< |
reference method, a full multipolar Ewald treatment. |
304 |
> |
reference method, a full multipolar Ewald treatment.\cite{Smith82,Smith98} |
305 |
|
|
306 |
|
|
307 |
|
%\subsection{Conservation of total energy } |
330 |
|
where the multipole operator for site $\bf a$, $\hat{M}_{\bf a}$, is |
331 |
|
expressed in terms of the point charge, $C_{\bf a}$, dipole, ${\bf D}_{\bf |
332 |
|
a}$, and quadrupole, $\mathbf{Q}_{\bf a}$, for object |
333 |
< |
$\bf a$. |
333 |
> |
$\bf a$, etc. |
334 |
|
|
335 |
|
% Interactions between multipoles can be expressed as higher derivatives |
336 |
|
% of the bare Coulomb potential, so one way of ensuring that the forces |
358 |
|
\label{generic} |
359 |
|
\end{equation} |
360 |
|
where $f_n(r)$ is a shifted kernel that is appropriate for the order |
361 |
< |
of the interaction, with $n=0$ for charge-charge, $n=1$ for |
362 |
< |
charge-dipole, $n=2$ for charge-quadrupole and dipole-dipole, $n=3$ |
363 |
< |
for dipole-quadrupole, and $n=4$ for quadrupole-quadrupole. To ensure |
364 |
< |
smooth convergence of the energy, force, and torques, a Taylor |
365 |
< |
expansion with $n$ terms must be performed at cutoff radius ($r_c$) to |
366 |
< |
obtain $f_n(r)$. |
361 |
> |
of the interaction (see Ref. \onlinecite{PaperI}), with $n=0$ for |
362 |
> |
charge-charge, $n=1$ for charge-dipole, $n=2$ for charge-quadrupole |
363 |
> |
and dipole-dipole, $n=3$ for dipole-quadrupole, and $n=4$ for |
364 |
> |
quadrupole-quadrupole. To ensure smooth convergence of the energy, |
365 |
> |
force, and torques, a Taylor expansion with $n$ terms must be |
366 |
> |
performed at cutoff radius ($r_c$) to obtain $f_n(r)$. |
367 |
|
|
368 |
|
% To carry out the same procedure for a damped electrostatic kernel, we |
369 |
|
% replace $1/r$ in the Coulomb potential with $\text{erfc}(\alpha r)/r$. |
403 |
|
connection to unmodified electrostatics as well as the smooth |
404 |
|
transition to zero in both these functions as $r\rightarrow r_c$. The |
405 |
|
electrostatic forces and torques acting on the central multipole due |
406 |
< |
to another site within cutoff sphere are derived from |
406 |
> |
to another site within the cutoff sphere are derived from |
407 |
|
Eq.~\ref{generic}, accounting for the appropriate number of |
408 |
|
derivatives. Complete energy, force, and torque expressions are |
409 |
|
presented in the first paper in this series (Reference |
417 |
|
shifted smoothly by finding the gradient for two interacting dipoles |
418 |
|
which have been projected onto the surface of the cutoff sphere |
419 |
|
without changing their relative orientation, |
420 |
< |
\begin{displaymath} |
420 |
> |
\begin{equation} |
421 |
|
U_{D_{\bf a}D_{\bf b}}(r) = U_{D_{\bf a}D_{\bf b}}(r) - |
422 |
|
U_{D_{\bf a} D_{\bf b}}(r_c) |
423 |
|
- (r_{ab}-r_c) ~~~\hat{r}_{ab} \cdot |
424 |
< |
\vec{\nabla} U_{D_{\bf a}D_{\bf b}}(r) \Big \lvert _{r_c} |
425 |
< |
\end{displaymath} |
424 |
> |
\nabla U_{D_{\bf a}D_{\bf b}}(r_c). |
425 |
> |
\end{equation} |
426 |
|
Here the lab-frame orientations of the two dipoles, $\mathbf{D}_{\bf |
427 |
|
a}$ and $\mathbf{D}_{\bf b}$, are retained at the cutoff distance |
428 |
|
(although the signs are reversed for the dipole that has been |
445 |
|
In general, the gradient shifted potential between a central multipole |
446 |
|
and any multipolar site inside the cutoff radius is given by, |
447 |
|
\begin{equation} |
448 |
< |
U^{\text{GSF}} = \sum \left[ U(\mathbf{r}, \hat{\mathbf{a}}, \hat{\mathbf{b}}) - |
449 |
< |
U(\mathbf{r}_c,\hat{\mathbf{a}}, \hat{\mathbf{b}}) - (r-r_c) \hat{r} |
450 |
< |
\cdot \nabla U(\mathbf{r},\hat{\mathbf{a}}, \hat{\mathbf{b}}) \Big \lvert _{r_c} \right] |
448 |
> |
U^{\text{GSF}} = \sum \left[ U(\mathbf{r}, \hat{\mathbf{a}}, \hat{\mathbf{b}}) - |
449 |
> |
U(r_c \hat{\mathbf{r}},\hat{\mathbf{a}}, \hat{\mathbf{b}}) - (r-r_c) \hat{\mathbf{r}} |
450 |
> |
\cdot \nabla U(r_c \hat{\mathbf{r}},\hat{\mathbf{a}}, \hat{\mathbf{b}}) \right] |
451 |
|
\label{generic2} |
452 |
|
\end{equation} |
453 |
|
where the sum describes a separate force-shifting that is applied to |
454 |
< |
each orientational contribution to the energy. |
454 |
> |
each orientational contribution to the energy. In this expression, |
455 |
> |
$\hat{\mathbf{r}}$ is the unit vector connecting the two multipoles |
456 |
> |
($a$ and $b$) in space, and $\hat{\mathbf{a}}$ and $\hat{\mathbf{b}}$ |
457 |
> |
represent the orientations the multipoles. |
458 |
|
|
459 |
|
The third term converges more rapidly than the first two terms as a |
460 |
|
function of radius, hence the contribution of the third term is very |
461 |
|
small for large cutoff radii. The force and torque derived from |
462 |
< |
equation \ref{generic2} are consistent with the energy expression and |
462 |
> |
Eq. \ref{generic2} are consistent with the energy expression and |
463 |
|
approach zero as $r \rightarrow r_c$. Both the GSF and TSF methods |
464 |
|
can be considered generalizations of the original DSF method for |
465 |
|
higher order multipole interactions. GSF and TSF are also identical up |
467 |
|
the energy, force and torque for higher order multipole-multipole |
468 |
|
interactions. Complete energy, force, and torque expressions for the |
469 |
|
GSF potential are presented in the first paper in this series |
470 |
< |
(Reference~\onlinecite{PaperI}) |
470 |
> |
(Reference~\onlinecite{PaperI}). |
471 |
|
|
472 |
|
|
473 |
|
\subsection{Shifted potential (SP) } |
481 |
|
effectively shifts the total potential to zero at the cutoff radius, |
482 |
|
\begin{equation} |
483 |
|
U^{\text{SP}} = \sum \left[ U(\mathbf{r}, \hat{\mathbf{a}}, \hat{\mathbf{b}}) - |
484 |
< |
U(\mathbf{r}_c,\hat{\mathbf{a}}, \hat{\mathbf{b}}) \right] |
484 |
> |
U(r_c \hat{\mathbf{r}},\hat{\mathbf{a}}, \hat{\mathbf{b}}) \right] |
485 |
|
\label{eq:SP} |
486 |
|
\end{equation} |
487 |
|
where the sum describes separate potential shifting that is done for |
574 |
|
and have been compared with the values obtained from the multipolar |
575 |
|
Ewald sum. In Monte Carlo (MC) simulations, the energy differences |
576 |
|
between two configurations is the primary quantity that governs how |
577 |
< |
the simulation proceeds. These differences are the most imporant |
577 |
> |
the simulation proceeds. These differences are the most important |
578 |
|
indicators of the reliability of a method even if the absolute |
579 |
|
energies are not exact. For each of the multipolar systems listed |
580 |
|
above, we have compared the change in electrostatic potential energy |
586 |
|
\subsection{Implementation} |
587 |
|
The real-space methods developed in the first paper in this series |
588 |
|
have been implemented in our group's open source molecular simulation |
589 |
< |
program, OpenMD,\cite{openmd} which was used for all calculations in |
589 |
> |
program, OpenMD,\cite{Meineke05,openmd} which was used for all calculations in |
590 |
|
this work. The complementary error function can be a relatively slow |
591 |
|
function on some processors, so all of the radial functions are |
592 |
|
precomputed on a fine grid and are spline-interpolated to provide |
793 |
|
|
794 |
|
\begin{figure} |
795 |
|
\centering |
796 |
< |
\includegraphics[width=0.6\linewidth]{energyPlot_slopeCorrelation_combined-crop.pdf} |
796 |
> |
\includegraphics[width=0.85\linewidth]{energyPlot_slopeCorrelation_combined.eps} |
797 |
|
\caption{Statistical analysis of the quality of configurational |
798 |
|
energy differences for the real-space electrostatic methods |
799 |
|
compared with the reference Ewald sum. Results with a value equal |
866 |
|
|
867 |
|
\begin{figure} |
868 |
|
\centering |
869 |
< |
\includegraphics[width=0.6\linewidth]{forcePlot_slopeCorrelation_combined-crop.pdf} |
869 |
> |
\includegraphics[width=0.6\linewidth]{forcePlot_slopeCorrelation_combined.eps} |
870 |
|
\caption{Statistical analysis of the quality of the force vector |
871 |
|
magnitudes for the real-space electrostatic methods compared with |
872 |
|
the reference Ewald sum. Results with a value equal to 1 (dashed |
880 |
|
|
881 |
|
\begin{figure} |
882 |
|
\centering |
883 |
< |
\includegraphics[width=0.6\linewidth]{torquePlot_slopeCorrelation_combined-crop.pdf} |
883 |
> |
\includegraphics[width=0.6\linewidth]{torquePlot_slopeCorrelation_combined.eps} |
884 |
|
\caption{Statistical analysis of the quality of the torque vector |
885 |
|
magnitudes for the real-space electrostatic methods compared with |
886 |
|
the reference Ewald sum. Results with a value equal to 1 (dashed |
938 |
|
|
939 |
|
\begin{figure} |
940 |
|
\centering |
941 |
< |
\includegraphics[width=0.6 \linewidth]{Variance_forceNtorque_modified-crop.pdf} |
941 |
> |
\includegraphics[width=0.65\linewidth]{Variance_forceNtorque_modified.eps} |
942 |
|
\caption{The circular variance of the direction of the force and |
943 |
|
torque vectors obtained from the real-space methods around the |
944 |
|
reference Ewald vectors. A variance equal to 0 (dashed line) |
970 |
|
energy over time, $\delta E_1$, and the standard deviation of energy |
971 |
|
fluctuations around this drift $\delta E_0$. Both of the |
972 |
|
shifted-force methods (GSF and TSF) provide excellent energy |
973 |
< |
conservation (drift less than $10^{-6}$ kcal / mol / ns / particle), |
973 |
> |
conservation (drift less than $10^{-5}$ kcal / mol / ns / particle), |
974 |
|
while the hard cutoff is essentially unusable for molecular dynamics. |
975 |
|
SP provides some benefit over the hard cutoff because the energetic |
976 |
|
jumps that happen as particles leave and enter the cutoff sphere are |
985 |
|
|
986 |
|
\begin{figure} |
987 |
|
\centering |
988 |
< |
\includegraphics[width=\textwidth]{newDrift_12.pdf} |
988 |
> |
\includegraphics[width=\textwidth]{newDrift_12.eps} |
989 |
|
\label{fig:energyDrift} |
990 |
|
\caption{Analysis of the energy conservation of the real-space |
991 |
|
electrostatic methods. $\delta \mathrm{E}_1$ is the linear drift in |
997 |
|
utilized the same real-space cutoff, $r_c = 12$\AA.} |
998 |
|
\end{figure} |
999 |
|
|
1000 |
+ |
\subsection{Reproduction of Structural Features\label{sec:structure}} |
1001 |
+ |
One of the best tests of modified interaction potentials is the |
1002 |
+ |
fidelity with which they can reproduce structural features in a |
1003 |
+ |
liquid. One commonly-utilized measure of structural ordering is the |
1004 |
+ |
pair distribution function, $g(r)$, which measures local density |
1005 |
+ |
deviations in relation to the bulk density. In the electrostatic |
1006 |
+ |
approaches studied here, the short-range repulsion from the |
1007 |
+ |
Lennard-Jones potential is identical for the various electrostatic |
1008 |
+ |
methods, and since short range repulsion determines much of the local |
1009 |
+ |
liquid ordering, one would not expect to see any differences in |
1010 |
+ |
$g(r)$. Indeed, the pair distributions are essentially identical for |
1011 |
+ |
all of the electrostatic methods studied (for each of the different |
1012 |
+ |
systems under investigation). Interested readers may consult the |
1013 |
+ |
supplementary information for plots of these pair distribution |
1014 |
+ |
functions. |
1015 |
|
|
1016 |
+ |
A direct measure of the structural features that is a more |
1017 |
+ |
enlightening test of the modified electrostatic methods is the average |
1018 |
+ |
value of the electrostatic energy $\langle U_\mathrm{elect} \rangle$ |
1019 |
+ |
which is obtained by sampling the liquid-state configurations |
1020 |
+ |
experienced by a liquid evolving entirely under the influence of the |
1021 |
+ |
methods being investigated. In figure \ref{fig:Uelect} we show how |
1022 |
+ |
$\langle U_\mathrm{elect} \rangle$ for varies with the damping parameter, |
1023 |
+ |
$\alpha$, for each of the methods. |
1024 |
+ |
|
1025 |
+ |
\begin{figure} |
1026 |
+ |
\centering |
1027 |
+ |
\includegraphics[width=\textwidth]{averagePotentialEnergy_r9_12.eps} |
1028 |
+ |
\label{fig:Uelect} |
1029 |
+ |
\caption{The average electrostatic potential energy, |
1030 |
+ |
$\langle U_\mathrm{elect} \rangle$ for the SSDQ water with ions as a function |
1031 |
+ |
of the damping parameter, $\alpha$, for each of the real-space |
1032 |
+ |
electrostatic methods. Top panel: simulations run with a real-space |
1033 |
+ |
cutoff, $r_c = 9$\AA. Bottom panel: the same quantity, but with a |
1034 |
+ |
larger cutoff, $r_c = 12$\AA.} |
1035 |
+ |
\end{figure} |
1036 |
+ |
|
1037 |
+ |
It is clear that moderate damping is important for converging the mean |
1038 |
+ |
potential energy values, particularly for the two shifted force |
1039 |
+ |
methods (GSF and TSF). A value of $\alpha \approx 0.18$ \AA$^{-1}$ is |
1040 |
+ |
sufficient to converge the SP and GSF energies with a cutoff of 12 |
1041 |
+ |
\AA, while shorter cutoffs require more dramatic damping ($\alpha |
1042 |
+ |
\approx 0.36$ \AA$^{-1}$ for $r_c = 9$ \AA). It is also clear from |
1043 |
+ |
fig. \ref{fig:Uelect} that it is possible to overdamp the real-space |
1044 |
+ |
electrostatic methods, causing the estimate of the energy to drop |
1045 |
+ |
below the Ewald results. |
1046 |
+ |
|
1047 |
+ |
These ``optimal'' values of the damping coefficient are slightly |
1048 |
+ |
larger than what were observed for DSF electrostatics for purely |
1049 |
+ |
point-charge systems, although a value of $\alpha=0.18$ \AA$^{-1}$ for |
1050 |
+ |
$r_c = 12$\AA appears to be an excellent compromise for mixed charge |
1051 |
+ |
multipole systems. |
1052 |
+ |
|
1053 |
+ |
\subsection{Reproduction of Dynamic Properties\label{sec:structure}} |
1054 |
+ |
To test the fidelity of the electrostatic methods at reproducing |
1055 |
+ |
dynamics in a multipolar liquid, it is also useful to look at |
1056 |
+ |
transport properties, particularly the diffusion constant, |
1057 |
+ |
\begin{equation} |
1058 |
+ |
D = \lim_{t \rightarrow \infty} \frac{1}{6 t} \langle \left| |
1059 |
+ |
\mathbf{r}(t) -\mathbf{r}(0) \right|^2 \rangle |
1060 |
+ |
\label{eq:diff} |
1061 |
+ |
\end{equation} |
1062 |
+ |
which measures long-time behavior and is sensitive to the forces on |
1063 |
+ |
the multipoles. For the soft dipolar fluid, and the SSDQ liquid |
1064 |
+ |
systems, the self-diffusion constants (D) were calculated from linear |
1065 |
+ |
fits to the long-time portion of the mean square displacement |
1066 |
+ |
($\langle r^{2}(t) \rangle$).\cite{Allen87} |
1067 |
+ |
|
1068 |
+ |
In addition to translational diffusion, orientational relaxation times |
1069 |
+ |
were calculated for comparisons with the Ewald simulations and with |
1070 |
+ |
experiments. These values were determined from the same 1~ns $NVE$ |
1071 |
+ |
trajectories used for translational diffusion by calculating the |
1072 |
+ |
orientational time correlation function, |
1073 |
+ |
\begin{equation} |
1074 |
+ |
C_l^\alpha(t) = \left\langle P_l\left[\hat{\mathbf{u}}_i^\gamma(t) |
1075 |
+ |
\cdot\hat{\mathbf{u}}_i^\gamma(0)\right]\right\rangle, |
1076 |
+ |
\label{eq:OrientCorr} |
1077 |
+ |
\end{equation} |
1078 |
+ |
where $P_l$ is the Legendre polynomial of order $l$ and |
1079 |
+ |
$\hat{\mathbf{u}}_i^\alpha$ is the unit vector of molecule $i$ along |
1080 |
+ |
axis $\gamma$. The body-fixed reference frame used for our |
1081 |
+ |
orientational correlation functions has the $z$-axis running along the |
1082 |
+ |
dipoles, and for the SSDQ water model, the $y$-axis connects the two |
1083 |
+ |
implied hydrogen atoms. |
1084 |
+ |
|
1085 |
+ |
From the orientation autocorrelation functions, we can obtain time |
1086 |
+ |
constants for rotational relaxation either by fitting an exponential |
1087 |
+ |
function or by integrating the entire correlation function. These |
1088 |
+ |
decay times are directly comparable to water orientational relaxation |
1089 |
+ |
times from nuclear magnetic resonance (NMR). The relaxation constant |
1090 |
+ |
obtained from $C_2^y(t)$ is normally of experimental interest because |
1091 |
+ |
it describes the relaxation of the principle axis connecting the |
1092 |
+ |
hydrogen atoms. Thus, $C_2^y(t)$ can be compared to the intermolecular |
1093 |
+ |
portion of the dipole-dipole relaxation from a proton NMR signal and |
1094 |
+ |
should provide an estimate of the NMR relaxation time |
1095 |
+ |
constant.\cite{Impey82} |
1096 |
+ |
|
1097 |
+ |
Results for the diffusion constants and orientational relaxation times |
1098 |
+ |
are shown in figure \ref{fig:dynamics}. From this data, it is apparent |
1099 |
+ |
that the values for both $D$ and $\tau_2$ using the Ewald sum are |
1100 |
+ |
reproduced with high fidelity by the GSF method. |
1101 |
+ |
|
1102 |
+ |
The $\tau_2$ results in \ref{fig:dynamics} show a much greater |
1103 |
+ |
difference between the real-space and the Ewald results. |
1104 |
+ |
|
1105 |
+ |
|
1106 |
|
\section{CONCLUSION} |
1107 |
|
In the first paper in this series, we generalized the |
1108 |
|
charge-neutralized electrostatic energy originally developed by Wolf |